I don't forsee this as game-breaking, but there are some considerations that raiding guilds need to bear in mind.
Does PvE Raiding Own Both Specs? Currently, LOKI requires people to show up to raids with the appropriate PvE spec for their class/role. Now - if I'm not the one tanking this boss, and I'm still in as DPS - do I need a PvE DPS spec, or can I swing by with a PvP build? Similarly, does our Feral Druid need to have a Bear spec, and a Cat spec? Rogue have a positional and non-positional dependent PvE DPS spec? Priest have a group healing (holy) and tank healing spec (disc)? You can see where I'm going.
Raid Invites. Do you plan on bringing someone to do two, completely different jobs on purpose? IE, a Shadow Priest that goes Holy for high healing requirement fights. If so, what role officer (if thats how you operate) determines whom to bring. Do you penalize people that only want / are able to play one spec? This also ties into...
Loot. How do you determine who gets what loot? Do single spec people get priority? Can everyone bid/spend DKP (if thats what you use) on all specs, only ones they raid with, or just a single spec?
Recruitment. Do you require people to have / play a second spec, have gear for multiple specs, and need to get applications passed through all officers that could end up working with that person?
Despite all the big questions, I think I've got a good handle on how LOKI will be running things. My instinct tells me that very little will change. Members will be associated with one spec, under that role's officer. People that previously had to respec between fights will take advantage of this system, and our core raiders will probably optimize both specs to do their job - though I doubt I'll require it (by nature of the players we accept, I doubt that people will not do everything possible to help progression). Loot will go to main specs first, with a cap on offspec gear bids - as gearing up one set of specs is all that people will really have a chance to do as we push progression. Second spec will be asked for in the application as a good-to-know thing, and in case we do need to shift someones spec permenently, but it won't make or break an app.
(Note to Guild Members: This is musings, not policy).